Assignment 7: Synthetic Biologygenetics.wustl.edu/bio5488/files/2017/03/StudentAssignment7_slide… · Assignment 7: Synthetic Biology March 3, 2017. Gene Synth. Goal of Assignment

Assignment7:SyntheticBiology

March3,2017

GeneSynth

GoalofAssignment

• Designprimerstosyntheticallyconstructanovelpeptide.• UseRecursiveFunctiontogenerateprimersequences

• Narrowdownprimersbasedonpreferredannealingtemperaturesandbyavoidingparticularrestrictionsites.• Booleansareadatatypewithtwovalues,TrueandFalseinpython.• Whenyouareusingan“if”statementyouarereallyevaluatingwhetherastatementisTrueorFalse.

Codontable

SincesomeAAshavemultiplecodonsequences,thecodemustbeabletogenerateallcombinationofsequencespossible.

BooleanExamples

>>>A=1ifA==1:(evaluatestoTrue)Dosomething

else:(abovewasFalse)Dosomethingelse

>>>A=10whileA>5:(EvaluatestoTruewhenAis10,9,8,7,6)(FalsewhenA=5)Print(A)A=A-1

>>>A=1A==2 evaluates toFalseA>1evaluates toFalseA<1evaluates toFalse0<Aevaluates toTrueTrueand Trueevaluates toTrueTrueand False evaluates toFalseFalse andFalse evaluates toFalseTrueand Trueevaluates toTruenotFalse evaluates toTruenotTrue evaluates toFalseFalse orTrueevaluates toTrueFalse orFalse evaluates toFalseTrueorTrue evaluates toTrue

Usingbooleans ->identifyparticularsequences

AnyandAllallowyoutosee ifastringappears inanotherstringorlistordictionary.• Anyactsasan“or”soFalseorFalseorTrueevaluatestoTrue.• Allactsasan“and”soFalse andFalseandTrueevaluates toFalse.

*Anytime aTrue isinan“or”statement,wholestatement isTrue.*Anytime aFalse isinan“and”statement,wholestatement isFalse.

Howtocalculatemeltingtemperature

MT=64.9+(41.0*(#G+#C- 16.4)/Lengthofoligo)

• Allprimersmustbewithin0.5degreesof58.0degreesCelsius!• Couldwriteanotherfunctionthatchecksforthis:

ie.def meltingtemp(DNA_seq):

Yourassignment

• Youaregivenafunction(PolkCode)thatconvertsaminoacidsequencestoallpossiblenucleotidesequences.• Given3AAsequences,youneedtofindnucleotideoutputsbasedwithinacertaintemperaturerangewithsequencerestrictions.• YourcodewilltakeAAsequence(s)andmeltingtemperature(Tm)asinputandoutputallnucleotidesequencesmeetingthecriteria.•Considermakingyourcodesothatincantakeanynumberofinputs.

Requirements

•DueWednesday(3/22/16) beforeclass.•Yoursubmissionfoldershouldcontain:

• modified Polk.py script(cantake ineither2ormorearguments)• README.txt filewithinstructions onhowtorunyourprogramandatableoftheDNAstrings andtemperatures foreachAAinputted.

• ShouldprintPrimersequences andMelting Temperature• Remembertocommentyourscript!